IdMapDiffCounts: The IdMapDiffCounts class

In IdMappingAnalysis: ID Mapping Analysis

Description

Package: IdMappingAnalysis
Class IdMapDiffCounts

Object
~~|
~~+--IdMapBase
~~~~~~~|
~~~~~~~+--IdMapDiffCounts

Directly known subclasses:

public static class IdMapDiffCounts
extends IdMapBase

The IdMapDiffCounts class handles statistics on IdMapDiff object. IdMapDiffCounts object encapsulates a data frame with row names corresponding to the primary IDs and 6 columns subdivided into pairs <match(TRUE/FALSE),count> each pair corresponding to the disjoint events <A-A*B,A*B,B-A*B>, where A and B are secondary ID lists for ID Maps A and B from the IdMapDiff object. The 'pairNames' attribute of the IdMapDiffCounts contains the names of the source ID Map pair from which the IdMapDiff object was created.

Usage

IdMapDiffCounts(idMapDiff=NULL, verbose=FALSE, ...)

Arguments

idMapDiff	The IdMapDiff on which IdMapDiffCounts is cretated. Default is NULL.
verbose	If TRUE enables diagnostic messages. Default is FALSE.
...	Not used.

Fields and Methods

Methods:

	getCompoundEvents	Get compound events.
	getCompoundGroups	Get counts for each compound event in IdMapDiffCounts.
	plot	Produce a fountain plot representing the quantitative relationship of the compound events.
	summary	Get a compaund event counts summary report.

Methods inherited from IdMapBase:
[, aligned, as.data.frame, dim, dimnames, getName, primaryIDs, primaryKey, secondaryKey

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

Author(s)

Alex Lisovich, Roger Day

Examples

 #get primary IDs from an msms experiment set
 IDs<-IdMapBase$primaryIDs(examples$msmsExperimentSet);

 #create JointIdMap object aligned by primaryIDs
 jointIdMap<-JointIdMap(examples$identDfList,primaryIDs=IDs);

 #create IdMapDiff object
 diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);

 # create IdMapDiffCounts object
 diffCounts<-IdMapDiffCounts(diffs);
 diffCounts[1:10,];
 

IdMappingAnalysis documentation built on Oct. 31, 2019, 3:30 a.m.